The Open PCR device is thermo-cycler that helps to create strands of DNA. PCR stands for polymerase chain reaction. The Open PCR consists of a heating lid that clamps down on mini test tubes that are held 16-tube PCR main heating block. It also has a cooling fan to help bring down the temperature when it is necessary in the running experiment. The Open PCR alternates between temperatures in order to properly separate deoxyribose nucleic acid (DNA) strands, let primers bind to these strands, and then finish replication of DNA. Then the process repeats for several cycles. The LED screen displays the temperature, the cycle number over how many cycles total, and the ETA time until the test in completed. It heats up to 110 degrees Celsius by default, while its cool temperature sits at 25 degrees Celsius.

The Open PCR device is thermo-cycler that helps to create strands of DNA. PCR stands for polymerase chain reaction. The Open PCR consists of a heating lid that clamps down on mini test tubes that are held 16-tube PCR main heating block. It also has a cooling fan to help bring down the temperature when it is necessary in the running experiment. The Open PCR alternates between temperatures in order to properly separate deoxyribose nucleic acid (DNA) strands, let primers bind to these strands, and then finish replication of DNA. Then the process repeats for several cycles. The LED screen displays the temperature, the cycle number over how many cycles total, and the ETA time until the test in completed. It heats up to 110 degrees Celsius by default, while its cool temperature sits at 25 degrees Celsius.

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The Open PCR device must be plugged into the wall (power source) and can be connected to a computer via a USB port. The device is controlled by a simple software on the computer, which allows for the temperatures and cycles to be changed as needed, as well as a start/end test button.

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'''Test Run'''

'''Test Run'''

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First test was an experimental run to be sure the machine was running properly. This test was conducted on October 25th, 2012 and the test was successful. <br>

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The first test was an experimental run to be sure the machine was running properly. Empty PCR test tubes were placed in the main heating block and the heating lid was shut closed. The Open PCR communicated efficiently with the computer, starting when the "start test" button was clicked. The Open PCR heated and cooled properly, therefore passing guideline markers that the device was running properly. <br>

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This test was conducted on October 25th, 2012 and the test was successful. <br>

<br><br>

<br><br>

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When the reaction is finished, the samples can be tested to see if the cancerous gene is present. As discussed before, the primer has to bind with a very specific section of the DNA to initiate replication (Adenine can only bind to Thymine and Guanine can only bind to Cytosine). If the DNA has been replicated exponentially and a large quantity of the target DNA now lies within your sample, you know that the specific primer matched with the DNA strand and the cancerous gene is present. If no replication has occurred and a small amount of DNA is still in the sample, however, you can conclude that the DNA is free of the cancer gene because the primer could not match up with the strand. That would make Taq Polymerase unable to bind and add the dNTPs so the DNA could be copied.

When the reaction is finished, the samples can be tested to see if the cancerous gene is present. As discussed before, the primer has to bind with a very specific section of the DNA to initiate replication (Adenine can only bind to Thymine and Guanine can only bind to Cytosine). If the DNA has been replicated exponentially and a large quantity of the target DNA now lies within your sample, you know that the specific primer matched with the DNA strand and the cancerous gene is present. If no replication has occurred and a small amount of DNA is still in the sample, however, you can conclude that the DNA is free of the cancer gene because the primer could not match up with the strand. That would make Taq Polymerase unable to bind and add the dNTPs so the DNA could be copied.

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When looking at the statistical significance of the data, Bayesian Reasoning was applied, which is p(CT)= (p(TC)*p(c))/((P(TC)*p(C))+(p(T~C)*p(~c)). The proportion of patients with positive results is the proportion of A compared to A+C, where the top is A and the bottom portion is A+C. If applied to a group of 10,000 patients, where 1% have cancer, 80% of people with cancer will get a positive result, and 9.6% will also get a positive result, we found that the frequency of this cancer: 80/(80+950) = 7.8%.

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When looking at the statistical significance of the data, Bayesian Reasoning was applied, which is: <math>P(CT) =\frac{P(TC)\, P(c)} {P(TC)\, P(c)+P(TC)\,P(c)}. \,</math> . The proportion of patients with positive results is the proportion of A compared to A+C, where the top is A and the bottom portion is A+C. If applied to a group of 10,000 patients, where 1% have cancer, 80% of people with cancer will get a positive result, and 9.6% will also get a positive result, we found that the frequency of this cancer: 80/(80+950) = 7.8%.

The first image is an unamplified template DNA sequence. The next image shows the DNA becoming denatured (separated) due to the high temperature of 95˚C. In the next image shows the the DNA strand being chilled to 57˚C, causing short primer pieces of DNA to bind to the two strands of the DNA at opposite ends of the sequence to then be amplified. Taq Polymerase then binds to the primers and extends them at a temperature of 72˚C. This process results two new double stranded copies of the original template DNA and the process is repeated multiple times to create many copies of the template strand.

The first image is an unamplified template DNA sequence. The next image shows the DNA becoming denatured (separated) due to the high temperature of 95˚C. In the next image shows the the DNA strand being chilled to 57˚C, causing short primer pieces of DNA to bind to the two strands of the DNA at opposite ends of the sequence to then be amplified. Taq Polymerase then binds to the primers and extends them at a temperature of 72˚C. This process results two new double stranded copies of the original template DNA and the process is repeated multiple times to create many copies of the template strand.

* '''Sample''' = Samples are the gene solutions of the 2 patients' DNA being tested for a cancer gene. A positive control and negative control are included for comparison reasons; a positive control should (to the best of our knowledge) test for the cancer gene, and the negative control should not have the cancer gene.

* '''Sample''' = Samples are the gene solutions of the 2 patients' DNA being tested for a cancer gene. A positive control and negative control are included for comparison reasons; a positive control should (to the best of our knowledge) test for the cancer gene, and the negative control should not have the cancer gene.

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* '''Integrated Density''' = <!--- Otherwise known as "INTEN", integrated density is the calculated "brightness" of the image. this is accomplished by adding up the image pixels and the "mean gray value" of every pixel. - explain what "integrated density" means and how you did background subtraction to get this value --->

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* '''Integrated Density''' = Otherwise known as "INTEN", integrated density is the calculated "brightness" of the image. This is accomplished by adding up the number of pixels in the image and the "mean gray value" of each pixel. Two measurements were taken: one of the water droplet and the background of the image. The integrated density of the background is subtracted from the integrated density of the water droplet. This calculation compensations for gravel and pixelation that is in the image caused by the Smartphone camera. When the background of the integrated density is subtracted, how well or brightly the image can be seen should remain.

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* '''DNA μg/mL''' = <!--- This is the concentration of DNA of micrograms per milliliters. This is calculated by the following equation: 2(Inten.--->

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* '''DNA μg/mL''' = This is the concentration of DNA of micrograms per milliliters. This is calculated by the following equation: 2(INTEN with subtracted background/DNA calf thymus with subtracted background). "INTEN" stands for integrated density, which is explained above. This equation allows for the calculation of concentration within the water droplet that was previously just a Smartphone image.

* '''Conclusion''' = A "positive" would mean the cancer gene is present in the DNA sample when comparing the concentration results with the positive control, which should contain the cancer gene and shows that it does by its concentration number. "No signal" would mean the DNA sample results reflected a negative for the cancer gene; the concentration of "No signal" samples should be significantly under the positive control's concentration displaying the cancer gene.

* '''Sample''' = <!--- explain what "integrated density" means and how you did background subtraction to get this value --->

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* '''Sample''' = Sample refers to what is in the test tubes. This includes the 2 patients' DNA that are being tested for the cancer gene. The positive and negative controls should, respectively, be positive for the cancer gene and negative for the cancer gene. The water blank is simply another negative control

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* '''BG''' = <!--- "BG" stands for background, which is the density --->

LAB 1 WRITE-UP

Initial Machine Testing

The Original Design

Description of Open PCR Device

The Open PCR device is thermo-cycler that helps to create strands of DNA. PCR stands for polymerase chain reaction. The Open PCR consists of a heating lid that clamps down on mini test tubes that are held 16-tube PCR main heating block. It also has a cooling fan to help bring down the temperature when it is necessary in the running experiment. The Open PCR alternates between temperatures in order to properly separate deoxyribose nucleic acid (DNA) strands, let primers bind to these strands, and then finish replication of DNA. Then the process repeats for several cycles. The LED screen displays the temperature, the cycle number over how many cycles total, and the ETA time until the test in completed. It heats up to 110 degrees Celsius by default, while its cool temperature sits at 25 degrees Celsius.

The Open PCR device must be plugged into the wall (power source) and can be connected to a computer via a USB port. The device is controlled by a simple software on the computer, which allows for the temperatures and cycles to be changed as needed, as well as a start/end test button.

Experimenting With the Connections

When we unplugged the LED from the Open PCR circuit board, the machine stop displaying information on the LED screen.

When we unplugged the white wire that connects the Open PCR circuit board to main heat sink, the machine incorrectly displays the temperature as negative 40 degrees Celsius.

Test Run

The first test was an experimental run to be sure the machine was running properly. Empty PCR test tubes were placed in the main heating block and the heating lid was shut closed. The Open PCR communicated efficiently with the computer, starting when the "start test" button was clicked. The Open PCR heated and cooled properly, therefore passing guideline markers that the device was running properly.

This test was conducted on October 25th, 2012 and the test was successful.

Protocols

Polymerase Chain Reaction

The Polymerase Chain Reaction is a process that relies on thermal cycling allowing the DNA to be broken apart and replicated. This biochemical process works by separating a strand of DNA allowing a primer to target and begin replicating a segment of DNA. This separation, replication, and amplification of a specific DNA strand occurs within the machine during the thermal cycling.

Procedure:

Obtain DNA samples and clearly lab each tube with the sample name.

50 μL of the PCR reaction mixture was added to each 50 μL sample of patient DNA. Three samples of each patient were prepared along with one sample each of a positive control and a negative control.

The eight prepared samples were placed into the PCR Machine, the lid must be screwed down until it rests on the test tubes.

The hydrophobic slide was placed onto the LED box and the first two rows of nodes were centered with the LED.

For each sample two drops of the Sybr Green Dye was added to the center nodes of the slide. One drop for each node, or until the two drops coalesced.

Two drops of the sample patient (or positive or negative control as appropriate) solution were added to the dye.

The LED was turned on and the phone camera was centered onto the drop, held up by the stand.

The dark box was placed over the whole setup and closed as completely as possible.

A picture was taken and sent to the ImageJ program to be analyzed.

The drop was removed and disposed of and the slide was re centered on the next two nodes.

The whole procedure was repeated for each sample with the phone in the same place in relation to the drop throughout the entire procedure.

ImageJ Procedure

Attach the image to an E-mail to be sent from the smart phone to the ImageJ Software Operator

Save the image to a computer with ImageJ software, opening the image to be analyzed.

In the ImageJ software open the analyze toolbar and mark the following boxes under Set Measurements: Area, Mean Grey Area Value, Integrated Density

Once the image is opened in ImageJ use the top drop down menu to select "Image" and then "Color" and then "Split Screen"

Only use the green channel, closing out the red and blue channel

Use the oval tool to select only the drop of liquid, getting as little background as possible while not cutting any of the drop out.

After selecting only the drop press Ctrl+M

Move the circle to the background image without changing the size by clicking and dragging the circle

Finally, save the results as an excel spreadsheet (set by default)

Fluorimeter Measurements

Image Number

Drop 1

Drop 2

1

Sybr Green

Calibration

2

Sybr Green

Positive Control

3

Sybr Green

Patient 1 Sample A

4

Sybr Green

Patient 1 Sample B

5

Sybr Green

Patient 1 Sample C

6

Sybr Green

Negative Control

7

Sybr Green

Patient 2 Sample A

8

Sybr Green

Patient 2 Sample B

9

Sybr Green

Patient 2 Sample C

10

Sybr Green

Water Blank

Research and Development

Specific Cancer Marker Detection - The Underlying Technology

To understand how a Polymerase Chain Reaction machine works, first an understanding of how DNA replicates in the human body must be explained. DNA must replicated to form new identical cells so that the organism the cells are supporting can grow and adapt to conditions it faces. The replication process is very complicated and involves a series of enzymes. In a nutshell, DNA begins with a double helix structure. Once unwound, by the enzyme helicase, the base pairs (Adenine, Thymine, Guanine, and Cytosine) that were held together by hydrogen bonds are now exposed and able to bind with free floating dNTPs with the help of DNA Polymerase III after a primer has been laid down.

The step of adding a primer is extremely important. Without an initial strand of RNA to allow DNA Polymerase III to bind, replication would not occur. This is extremely important for our experiment involving the PCR machine. We are testing to see if a cancer gene is present in patients, and without the initial DNA primer being able to bind, we can tell if the cancerous genes are present in that person because the DNA would not be amplified. More on that later.

When using an Open PCR (Polymerase Chain Reaction) machine for the first time, you must first make sure that you have a computer capable of running the software and download it. After the software is loaded, plug in the Open PCR machine and prepare your DNA samples that were submitted to be tested for the cancer marker. First, you must prepare the samples for amplification by adding the sample DNA, Taq Polymerase (for replication), MgCl2, and the dNTPs. This experiment focused on identifying a cancer associated gene (rs17879961) that was the result of a missense mutation (a change in the sequence ATT to ACT) which would cause the protein transcribed to become threonine instead of isoleucine. That sequence is related to patients getting Breast Cancer and Colorectal Cancer. The DNA primer being used for the detection of this cancer sequence is going to be AAACTCTTACACTGCATACA, which has the missense mutation within it. The way to know if the sample DNA has a positive result for the cancer gene is if amplification occurs. The primer will bind to the DNA if the cancer sequence is present and the strands will replicate exponentially, whereas if the cancer marker is not present, the primer will not bind to the DNA and it will not replicate because Taq Polymerase will not be able to bind. After the samples are prepared for amplification, the PCR program must be set up. To mimic the replication process of DNA in human cells, we manipulate the system by adding Taq Polymerase instead of DNA Polymerase III because the Taq Polymerase is heat resistant, and heat is going to be used to take place of the enzymes that originally initiate and carry out the DNA replication process. The temperatures that need to be programmed into the PCR are 95˚C (separates the DNA strands to prepare for replication), 57˚C (causes the primers to bind to the DNA), and 72˚C (causes Taq Polymerase to be initiated). There should be 30 cycles entered into this program to make sure ample amplification has occurred. After the 30 cycles are complete, the user can take out the sample and freeze them for later use.

When the reaction is finished, the samples can be tested to see if the cancerous gene is present. As discussed before, the primer has to bind with a very specific section of the DNA to initiate replication (Adenine can only bind to Thymine and Guanine can only bind to Cytosine). If the DNA has been replicated exponentially and a large quantity of the target DNA now lies within your sample, you know that the specific primer matched with the DNA strand and the cancerous gene is present. If no replication has occurred and a small amount of DNA is still in the sample, however, you can conclude that the DNA is free of the cancer gene because the primer could not match up with the strand. That would make Taq Polymerase unable to bind and add the dNTPs so the DNA could be copied.

When looking at the statistical significance of the data, Bayesian Reasoning was applied, which is: . The proportion of patients with positive results is the proportion of A compared to A+C, where the top is A and the bottom portion is A+C. If applied to a group of 10,000 patients, where 1% have cancer, 80% of people with cancer will get a positive result, and 9.6% will also get a positive result, we found that the frequency of this cancer: 80/(80+950) = 7.8%.

The first image is an unamplified template DNA sequence. The next image shows the DNA becoming denatured (separated) due to the high temperature of 95˚C. In the next image shows the the DNA strand being chilled to 57˚C, causing short primer pieces of DNA to bind to the two strands of the DNA at opposite ends of the sequence to then be amplified. Taq Polymerase then binds to the primers and extends them at a temperature of 72˚C. This process results two new double stranded copies of the original template DNA and the process is repeated multiple times to create many copies of the template strand.

Results

Water Drop

Calf Thymus DNA

Sample

Integrated Density

DNA μg/mL

Conclusion

PCR: Negative Control

2980332

0.5449091318

No Signal

PCR: Positive Control

12138637

2.219368

Positive

PCR: Patient 1 ID 64129, Rep 1

5320075

0.912696

No Signal

PCR: Patient 1 ID 64129, Rep 2

3769062

0.6891166

No Signal

PCR: Patient 1 ID 64129, Rep 3

2996412

0.547849

No Signal

PCR: Patient 2 ID 53409, Rep 1

4731227

0.865034096

No Signal

PCR: Patient 2 ID 53409, Rep 2

6332582

1.1578179076

No Signal

PCR: Patient 2 ID 53409, Rep 3

5511982

1.0077834706

No Signal

KEY

Sample = Samples are the gene solutions of the 2 patients' DNA being tested for a cancer gene. A positive control and negative control are included for comparison reasons; a positive control should (to the best of our knowledge) test for the cancer gene, and the negative control should not have the cancer gene.

Integrated Density = Otherwise known as "INTEN", integrated density is the calculated "brightness" of the image. This is accomplished by adding up the number of pixels in the image and the "mean gray value" of each pixel. Two measurements were taken: one of the water droplet and the background of the image. The integrated density of the background is subtracted from the integrated density of the water droplet. This calculation compensations for gravel and pixelation that is in the image caused by the Smartphone camera. When the background of the integrated density is subtracted, how well or brightly the image can be seen should remain.

DNA μg/mL = This is the concentration of DNA of micrograms per milliliters. This is calculated by the following equation: 2(INTEN with subtracted background/DNA calf thymus with subtracted background). "INTEN" stands for integrated density, which is explained above. This equation allows for the calculation of concentration within the water droplet that was previously just a Smartphone image.

Conclusion = A "positive" would mean the cancer gene is present in the DNA sample when comparing the concentration results with the positive control, which should contain the cancer gene and shows that it does by its concentration number. "No signal" would mean the DNA sample results reflected a negative for the cancer gene; the concentration of "No signal" samples should be significantly under the positive control's concentration displaying the cancer gene.

Sample

Area

Mean

Raw Integrated Density

Patient: 64129, Rep 1

120426

47.458

5715170

Patient: 64129, Rep 1 (BG)

120426

3.281

395095

Patient: 64129, Rep 2

104396

38.328

4001251

Patient: 64129, Rep 2 (BG)

104396

2.224

232182

Patient: 64129, Rep 3

126702

27.463

3479586

Patient: 64129, Rep 3 (BG)

126702

3.813

483174

Patient: 53409, Rep 1

105038

47.476

4986790

Patient: 53409, Rep 1 (BG)

105038

2.433

255563

Patient: 53409, Rep 2

111698

58.961

6585858

Patient: 53409, Rep 2 (BG)

111698

2.268

253276

Patient: 53409, Rep 3

114600

50.648

5804245

Patient: 53409, Rep 3 (BG)

114600

2.55

292263

Negative Control

150301

22.966

3451847

Negative Control (BG)

150301

3.137

471515

Blank - Water

135425

29.629

4012574

Blank - Water (BG)

135425

2.721

368551

Positive Control

94416

131.113

12379192

Positive Control (BG)

94416

2.548

240555

KEY

Sample = Sample refers to what is in the test tubes. This includes the 2 patients' DNA that are being tested for the cancer gene. The positive and negative controls should, respectively, be positive for the cancer gene and negative for the cancer gene. The water blank is simply another negative control

BG = "BG" stands for background density of the image.

Area = Number of pixels in the image; part of the calculation for integrated density.

Mean = The "mean gray area" of each pixels; part of the calculation for integrated density.

Raw Integrated Density = This is the integrated density without the background subtracted.